scholarly journals Molecular characterization of the intestinal microbiota in patients with and without abdominal bloating

2016 ◽  
Vol 310 (6) ◽  
pp. G417-G426 ◽  
Author(s):  
Tamar Ringel-Kulka ◽  
Andrew K. Benson ◽  
Ian M. Carroll ◽  
Jaehyoung Kim ◽  
Ryan M. Legge ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Abdominal Bloating ◽  
Well Differentiated ◽  
Irritable Bowel ◽  
The Relationship ◽  
The 16S Rrna Gene

Recent studies have demonstrated differences in the intestinal microbiota between patients with irritable bowel syndrome (IBS) and healthy controls (HC), suggesting a role for the intestinal microbiota in the pathogenesis of IBS. Alterations in the microbiota have also been implicated in the pathogenesis of abdominal bloating, a commonly reported symptom in IBS. We investigated the relationship between the intestinal microbiota, abdominal bloating, and altered bowel patterns in a cohort of patients with IBS and HC. The 16S rRNA gene from fresh fecal samples was amplified and pyrosequenced by using Roche-454 Titanium chemistry. A Core Measurable Microbiome (CMM) was generated for Operational Taxonomic Unit (OTU) detected in >75% of all samples and compositional features of CMM were compared between groups by Linear Discriminant Analysis (LDA). IBS differentiated from HC by LDA using continuous variation in the species/OTUs or the CMM genera. When subcategorized based on bloating symptoms and bowel characteristics, the same subjects were also well differentiated from one another and from HC. ANOVA analysis showed quantitative species/OTU differences between the subgroups including IBS with and without bloating, and subtypes based on bowel characteristics. The clear LDA differentiation and the significant microbial taxa differences between the groups imply a significant association of the microbiota with bloating symptoms and bowel characteristics in IBS. These changes in the microbiota may serve as a biomarker for IBS and its clinical subtypes and suggest a role for the intestinal microbiota in the pathogenesis of the main symptoms of the disorder.

The Gut Microbiota and Seleno-Compound as Emerging Risk Factors for Acute Myocardial Infarction

2021 ◽  
Author(s):  
Chin-Feng Tsai ◽  
Pang-Shuo Huang ◽  
Ching-Yu Shih ◽  
Mong-Hsun Tsai ◽  
Juey-Jen Hwang ◽  
...  
Keyword(s):  
Variable Region ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Emerging Risk ◽  
Genomic Dnas ◽  
The Relationship ◽  
The 16S Rrna Gene

Abstract BackgroundIt has been seemed that the gut microbiome alterations might be proposed as the metabolic disorder. However, the relationship between the microbiome and AMI has not been well validated. Methods The feces of the 44 subjects (AMI: 19; control: 25) were collected for fecal genomic DNAs extraction. The variable region V3–V4 of the 16S rRNA gene was sequencing by the platform of Illumina Miseq. The abundances of metabolites were analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. ResultsThe abundance of bacteria was more enriched in the AMI group both in the observed operational taxonomic units (OTUs) and faith phylogenetic diversity (PD) (p-value=0.01 and <0.001 with 95% CI, individually). Selenomonadales was less enriched in the AMI group at the Family, Genus, and Species levels [all linear discriminant analysis (LDA) scores >2]. The seleno-compound was more abundant in the AMI group at the Family, Genus, and Species levels (all LDA scores >2).Conclusions This is the first study to demonstrate Selenomonadales and seleno-compound to be associated with the occurrence of AMI. Our findings provide an opportunity for a novel prevention and treatment of AMI.

scholarly journals Red Cusk-Eel (Genypterus chilensis) Gut Microbiota Description of Wild and Aquaculture Specimens

2022 ◽  
Vol 10 (1) ◽  
pp. 105
Author(s):  
Jaime Romero ◽  
Osmán Díaz ◽  
Claudio D. Miranda ◽  
Rodrigo Rojas
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Acid Synthesis ◽  
Intestinal Content ◽  
Meat Production ◽  
Rrna Gene ◽  
Potential Contribution ◽  
Ion Torrent ◽  
The 16S Rrna Gene ◽  
Genypterus Chilensis

Chile has promoted the diversification of aquaculture and red cusk-eel (Genypterus chilensis) is one of the prioritized species. However, many aspects of the biology of the species are unknown or have little information available. These include intestinal microbiota, an element that may play an important role in the nutrition and defense of cultured animals for meat production. This study compares the microbiota composition of the intestinal contents of wild and aquaculture fish to explore the microbial communities present and their potential contribution to the host. DNA was extracted from the intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the Ion Torrent platform. After the examination of the sequences, strong differences were found in the composition at the level of phylum, being Firmicutes and Tenericutes the most abundant in aquaculture and wild condition, respectively. At the genus level, the Vagococcus (54%) and Mycoplasma (97%) were the most prevalent in the microbial community of aquaculture and wild condition, respectively. The evaluation of predicted metabolic pathways in these metagenomes showed that in wild condition there is an important presence of lipid metabolism belonging to the unsaturated fatty acid synthesis. In the aquaculture condition, the metabolism of terpenoids and polyketides were relevant. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of red cusk-eel (Genypterus chilensis) of wild and aquaculture origin using high-throughput sequencing.

scholarly journals Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

Detection and Characterization of a Multi-drug and Multi-metal Resistant Enterobacterium Pantoea sp. from Tannery Wastewater after Secondary Treatment Process

2016 ◽  
Vol 2 (1 and 2) ◽  
pp. 37-42 ◽  
Author(s):  
Ashutosh Yadav ◽  
Abhay Raj ◽  
Ram Naresh Bharagava
Keyword(s):  
Toxic Metal ◽  
Tannery Wastewater ◽  
Contaminated Sites ◽  
Diffusion Method ◽  
Rrna Gene ◽  
Disk Diffusion Method ◽  
Gene Sequence Analysis ◽  
Nutrient Agar Medium ◽  
The 16S Rrna Gene

In this study, an enterobacterium was isolated from treated tannery wastewater and characterized as gram-negative, rod shaped, motile, and lactose fermenting bacterium. Further, based on the 16S rRNA gene sequence analysis, the bacterium was identified as Pantoea sp. with accession number The antibiotic and heavy KJ576899. metal resistant property of isolated bacterium was investigated by the disk diffusion method on Muller-Hinton and nutrient agar medium amended with the increasing concentrations of various toxic metal ions, respectively. Results showed that the isolated bacterium was sensitive for amikacin, ampicillin, cefepime, cetriaxone, chloramphenicol, levofloxacin, meropenem, nalidixic acid, piperacillin and tobramycin, resistant for aztreonam, carbenicillin, cefotaxime, ceftazidime, ciprofloxacin, cotrimoxazole, imepenam, moxifloxacin, streptomycin and tetracycline, but intermediate for amoxicillin and gentamicin. In addition, the bacterium also showed the Minimum Inhibitory Concentration (MIC) values of 250, 500, 160, 190, 600, 700, 500, 380, 600 and 350 μg ml-1 forCu, Cr, Cd, Co, Zn, Fe, Ni, Pb, Mo and As, respectively with a plasmid DNA of 33.5 kb. This multi-drug and multi-metal resistant bacterium can be used as a potential agent for the bioremediation of metal contaminated sites.

scholarly journals Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1400-1405 ◽  
Author(s):  
Abhishek Chari ◽  
Kelly F. Oakeson ◽  
Shinichiro Enomoto ◽  
D. Grant Jackson ◽  
Mark A. Fisher ◽  
...  
Keyword(s):  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Sodalis Glossinidius ◽  
Large Gene ◽  
Close Relationship ◽  
Metabolic Properties ◽  
Insect Symbionts ◽  
The 16S Rrna Gene

A Gram-stain-negative bacterium, isolated from a human wound was previously found to share an unprecedentedly close relationship with Sodalis glossinidius and other members of the Sodalis-allied clade of insect symbionts. This relationship was inferred from sequence analysis of the 16S rRNA gene and genomic comparisons and suggested the strain belonged to a novel species. Biochemical and genetic analyses supported this suggestion and demonstrated that the organism has a wide repertoire of metabolic properties, which is consistent with the presence of a relatively large gene inventory. Among members of the Sodalis-allied clade, this is the first representative that has sufficient metabolic capabilities to sustain growth in minimal media. On the basis of the results of this study, we propose that this organism be classified as a representative of a novel species, Sodalis praecaptivus sp. nov. (type strain HST = DSM 27494T = ATCC BAA-2554T).

Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean

2007 ◽  
Vol 57 (8) ◽  
pp. 1815-1818 ◽  
Author(s):  
Kiyoung Lee ◽  
Yoe-Jin Choo ◽  
Stephen J. Giovannoni ◽  
Jang-Cheon Cho
Keyword(s):  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Sargasso Sea ◽  
Bacterial Strains ◽  
Ruegeria Pomeroyi ◽  
Distinct Line ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Gram-negative, facultatively aerobic, chemoheterotrophic, short rod-shaped marine bacterial strains HTCC2662T and HTCC2663, isolated from the Sargasso Sea by using a dilution-to-extinction culturing method, were investigated to determine their taxonomic position. Characterization of the two strains by phenotypic and phylogenetic analyses revealed that they belonged to the same species. The DNA G+C content of strain HTCC2662T was 58.4 mol% and the predominant cellular fatty acids were C18 : 1 ω7c (52.5 %), C16 : 0 2-OH (13.5 %) and C18 : 1 11-methyl ω7c (12.2 %). Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains represented a distinct line of descent within the genus Ruegeria, with highest sequence similarities to Ruegeria atlantica DSM 5823T (97.2 %), Ruegeria lacuscaerulensis DSM 11314T (96.5 %) and Ruegeria pomeroyi DSM 15171T (95.6 %). Several phenotypic characteristics, including facultatively requiring NaCl and oxygen for growth, together with the cellular fatty acid composition, differentiated strain HTCC2662T from other members of the genus Ruegeria. Based on phenotypic, chemotaxonomic and phylogenetic traits, it is suggested that strains HTCC2662T and HTCC2663 represent a novel species of the genus Ruegeria, for which the name Ruegeria pelagia sp. nov. is proposed. The type strain is HTCC2662T (=KCCM 42378T=NBRC 102038T).

scholarly journals MOLECULAR CHARACTERIZATION OF GENE 16S rRNA MICRO SYMBIONTS IN SPONGE AT MELAWAI BEACH, EAST KALIMANTAN

2018 ◽  
Author(s):  
Ismail Marzuki ◽  
Alfian Noor ◽  
Nursiah La Nafie
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Isolation And Purification ◽  
East Kalimantan ◽  
Degree Of Similarity ◽  
The 16S Rrna Gene

Molecular characterization studies have been conducted 16S rRNA gene micro symbiont of sponge origin Melawai Beach, Balikpapan in East Kalimantan. Objective analysis of histo- morphological research, isolation-purification, molecular characterization of micro-symbiont genes in order to search symbiont bacteria that can live in extreme environments contaminated hydrocarbon waste. The research method that morphological identification, isolation-purification and molecular characterization of the 16S rRNA gene with Chain Reaction Polymerization method. The results of histo-morphological analysis concluded sponge samples with species of Callyspongia sp. Isolation and purification mikro symbionts of sponge obtained 2 (two) isolates. Characteristics of Isolates 1; spherical shape, colonize and creamy, while isolates 2; jagged shape, oval and white colonies. Molecular characterization of the 16S rRNA gene by PCR, Bacillus subtilis strain BAB-684 identification for isolates one is the number of nucleotide pairs reached 899 bp and the degree of similarity in GenBank reached 89% homologous, while the second is a Bacillus flexus strain PHCDB20 isolates the number reached 950 bp nucleotide pairs with the degree of similarity in GenBank reached 99% homologous

scholarly journals Dynamic changes in intestinal microbiota in young forest musk deer during weaning

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8923
Author(s):  
Yimeng Li ◽  
Minghui Shi ◽  
Tianxiang Zhang ◽  
Xin Hu ◽  
Baofeng Zhang ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Relative Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Musk Deer ◽  
Dynamic Changes ◽  
Linear Discriminant ◽  
Bacterial Phyla ◽  
Young Forest ◽  
Rrna Gene Sequencing

Weaning is an important event for all mammals, including young forest musk deer. However, weaning stress may cause intestinal microbiota-related disorders. Therefore, high-throughput 16S rRNA gene sequencing was applied to study the dynamic changes in intestinal microbiota during pre-weaning (10 days before weaning) and post-weaning (10 days after weaning) in 15 young forest musk deer. We saw that intestinal microbiota diversity in the post-weaning period was significantly higher than that in the pre-weaning period. The most dominant bacterial phyla were similar in the two groups (Firmicutes, Bacteroidetes and Verrucomicrobia). Meanwhile, we applied Linear discriminant analysis effect size (LefSe) to identify the most differentially microbial taxa in the pre-weaning and post-weaning groups. In the post-weaning forest musk deer, the relative abundance of Actinobacteria, Spirochaetes, Ruminococcaceae_UCG-005, Treponema and Prevotella was higher than in the pre-weaning group. However, higher relative abundance of the phyla Bacteroidetes was found in the pre-weaning group compared with that in the post-weaning group. In summary, this research provides a theoretical foundation for the dynamics of young forest musk deer intestinal microbiota during the weaning transition, which may benefit in understanding the growth and health of forest musk deer.

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